A PhD-position in Environmental Genomics is available at the Department of Ecological Science, for the research project entitled ‘Dose-response Curves for –OMICS data in soil quality assessment (DrCOMICS)’, funded by the NWO division ‘Toegepaste en Technische Wetenschappen (TTW)’. Within this project we aim to develop a dose-response analysis tool for –omics data using Bayesian statistics. To that end, the candidate will perform stress-response experiments under controlled laboratory conditions as well as under field conditions to generate –omics, pathway and phenotypic response data over a large range of stress intensities with high statistical power. Dose-response modelling will be developed using Bayesian statistics in collaboration with the group of Prof. dr. Heskes from the Institute for Computing and Information Science (ICIS), Radboud University Nijmegen. Eventually, we aim to apply this methodology to develop and validate indicators to assess environmental quality from -omics data. As case study, we will focus on the effects of neonicotinoids on soil quality using the model Folsomia candida.

Tasks
• Ecotoxicological experiments using model species Folsomia candida in order to quantify phenotypic effects of neonicotinoids;
• conduct exposures at sub-lethal effect concentrations over a large range of neonicotinoid exposure concentrations;
• RNA-, Protein and metabolite isolation for  transcriptome- proteome and metabolome analysis;
• library preparation (Illumina Truseq) for Next generation sequencing
• Coupled liquid chromatography/mass spectrometry (LC-MS) analysis. 
• Bioinformatics, statistical analysis of transcript-, protein- and metabolite abundance
• writing of scientific manuscripts and a PhD-thesis at the end of the project.

• MSc in Biomolecular Sciences or comparable, with relevant research experience;
• experience with Bioinformatics (e.g. MSc internship on this topic) is essential;
• excellent social skills to work in an interdisciplinary national research team;
• English language proficiency.

The appointment will be initially for 1 year. After satisfactory evaluation of the initial appointment, it can be extended for a total duration of 4 years. About 75% of the time is devoted to research, the remaining 25% to education and assistance in courses. The education program is organized by the national research school on Environmental Science (SENSE).
You can find information about our excellent fringe benefits of employment at www.workingatvu.nl like:
• Remuneration of 8,3% end-of-year bonus and 8% holiday allowance;
• A minimum of 29 holidays In case of full-time employment;
• A wide range of sports facilities, which staff may use at a modest charge;
•Generous contribution (65%) commuting allowance based on public transport. 
   
The salary will be in accordance with university regulations for academic personnel, and ranges from a minimum of € 2.222 gross per month up to a maximum of € 2.840 gross per month based on fulltime employment (salary scale 85) for a PhD student. 
 

Vrije Universiteit Amsterdam

Vrije Universiteit Amsterdam (VU) is a leading, innovative and growing university that is at the heart of society and actively contributes to new developments in teaching and research. Our university has ten faculties, and provides work for over 4,500 staff and scientific education for more than 23,000 students.

The Department of Ecological Science (DES) answers fundamental ecological and evolutionary questions regarding the relationship between organisms and their environment at the full array of hierarchical levels: from molecular ecology to ecosystem research. The department comprises a dynamic community of researchers and provides an excellent research environment with state-of-the-art facilities and high quality training.